This directory contains a dump of the UCSC genome annotation database for
the Oct. 2011 (FUGU5/fr3) assembly of the fugu genome
(fr3, Fugu Genome Sequencing Consortium - FUGU5
(NCBI project 1434, GCA_000180615.2)).
The annotations were generated by UCSC and collaborators worldwide.

This assembly was produced by the Fugu Genome Sequencing Consortium,
               http://www.fugu-sg.org/
as part of the International Fugu Genome Consortium, led by JGI and the
Singapore Institute of Molecular and Cell Biology (IMCB).

For more information on the fugu genome, see the project website:
       http://www.fugu-sg.org/

Files included in this directory (updated nightly):

  - *.sql files:  the MySQL commands used to create the tables

  - *.txt.gz files: the database tables in a tab-delimited format
    compressed with gzip.

To see descriptions of the tables underlying Genome Browser annotation
tracks, select the table in the Table Browser:
  http://genome.ucsc.edu/cgi-bin/hgTables?db=fr3
and click the "describe table schema" button.  There is also a "view
table schema" link on the configuration page for each track.

---------------------------------------------------------------
If you plan to download a large file or multiple files from this 
directory, we recommend you use ftp rather than downloading the files 
via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then go to 
the directory goldenPath/fr3/database/. To download multiple 
files, use the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 

Alternate methods to ftp access.

Using an rsync command to download the entire directory:
    rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/fr3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/fr3/database/gc5BaseBw.txt.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/fr3/database/*'
With wget, a single file: 
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/fr3/database/gc5BaseBw.txt.gz' 
        -O gc5BaseBw.txt.gz

Please note that some files contents, such as this example gc5BaseBw.txt.gz,
will point to the data being hosted in another /gbdb/ location, which
refers to ftp://hgdownload.cse.ucsc.edu/gbdb/

To uncompress the *.txt.gz files:
    gunzip <table>.txt.gz
The tables can be loaded directly from the .txt.gz compressed file.
It is not necessary to uncompress them to load into a database,
as shown in the example below.

To load one of the tables directly into your local mirror database,
for example the table chromInfo:
## create table from the sql definition
$ hgsql fr3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql fr3 --local-infile=1 
        -e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'


==============================================================================

All the files and tables in this directory are freely usable for any purpose.

1.  These data have been freely provided by the JGI for use in the
        UCSC Genome Browser.

==============================================================================
      Name                         Last modified      Size  Description
Parent Directory - xenoMrna.txt.gz 2020-08-19 09:10 192M xenoMrna.sql 2020-08-19 09:10 2.1K windowmaskerSdust.txt.gz 2012-05-13 21:04 15M windowmaskerSdust.sql 2012-05-13 21:04 1.4K ucscToRefSeq.txt.gz 2018-02-18 06:31 52K ucscToRefSeq.sql 2018-02-18 06:31 1.4K ucscToINSDC.txt.gz 2019-02-10 03:41 50K ucscToINSDC.sql 2019-02-10 03:41 1.4K trackDb_pushedout.txt.gz 2023-12-05 13:51 43K trackDb_pushedout.sql 2023-12-05 13:51 2.1K trackDb.txt.gz 2023-12-05 13:51 43K trackDb.sql 2023-12-05 13:51 2.1K tableList.txt.gz 2024-04-14 03:31 4.9K tableList.sql 2024-04-14 03:31 1.6K tableDescriptions.txt.gz 2024-04-13 02:03 7.6K tableDescriptions.sql 2024-04-13 02:03 1.4K simpleRepeat.txt.gz 2012-05-13 20:53 3.4M simpleRepeat.sql 2012-05-13 20:53 1.9K seqNcbiRefSeq.txt.gz 2018-02-09 14:05 505K seqNcbiRefSeq.sql 2018-02-09 14:05 1.6K rmsk.txt.gz 2012-05-13 21:07 4.7M rmsk.sql 2012-05-13 21:07 1.8K refSeqAli.txt.gz 2020-08-19 09:23 49K refSeqAli.sql 2020-08-19 09:23 2.1K refGene.txt.gz 2020-08-19 09:22 47K refGene.sql 2020-08-19 09:22 1.9K refFlat.txt.gz 2020-08-19 09:22 42K refFlat.sql 2020-08-19 09:22 1.7K phyloP8way.txt.gz 2012-05-13 20:47 11M phyloP8way.sql 2012-05-13 20:47 1.7K phastConsElements8way.txt.gz 2012-05-13 21:07 11M phastConsElements8way.sql 2012-05-13 21:07 1.5K phastCons8way.txt.gz 2012-05-13 20:49 9.6M phastCons8way.sql 2012-05-13 20:49 1.7K netXenTro9.txt.gz 2017-12-14 10:21 4.9M netXenTro9.sql 2017-12-14 10:21 2.1K netTetNig2.txt.gz 2012-05-13 20:51 17M netTetNig2.sql 2012-05-13 20:50 2.0K netOryLat2.txt.gz 2012-05-13 21:05 12M netOryLat2.sql 2012-05-13 21:05 2.0K netOreNil1.txt.gz 2012-05-13 21:01 11M netOreNil1.sql 2012-05-13 21:01 2.0K netMm10.txt.gz 2013-08-04 13:04 4.8M netMm10.sql 2013-08-04 13:04 2.1K netLatCha1.txt.gz 2012-05-13 20:49 5.8M netLatCha1.sql 2012-05-13 20:49 2.0K netGasAcu1.txt.gz 2012-05-13 20:53 13M netGasAcu1.sql 2012-05-13 20:53 2.0K netGalGal6.txt.gz 2019-01-20 08:23 5.0M netGalGal6.sql 2019-01-20 08:23 2.1K netGadMor1.txt.gz 2012-05-13 21:04 9.8M netGadMor1.sql 2012-05-13 21:04 2.0K netDanRer7.txt.gz 2012-05-13 20:53 8.3M netDanRer7.sql 2012-05-13 20:53 2.0K nestedRepeats.txt.gz 2012-05-13 20:51 298K nestedRepeats.sql 2012-05-13 20:51 1.9K ncbiRefSeqPsl.txt.gz 2018-02-09 13:38 2.9M ncbiRefSeqPsl.sql 2018-02-09 13:38 2.1K ncbiRefSeqPredicted.txt.gz 2018-02-09 13:38 2.4M ncbiRefSeqPredicted.sql 2018-02-09 13:38 2.0K ncbiRefSeqPepTable.txt.gz 2018-02-09 14:05 7.9M ncbiRefSeqPepTable.sql 2018-02-09 14:05 1.4K ncbiRefSeqOther.txt.gz 2018-02-09 14:05 71 ncbiRefSeqOther.sql 2018-02-09 14:05 1.3K ncbiRefSeqLink.txt.gz 2018-02-09 13:38 1.0M ncbiRefSeqLink.sql 2018-02-09 13:38 2.0K ncbiRefSeqCurated.txt.gz 2018-02-09 13:38 42K ncbiRefSeqCurated.sql 2018-02-09 13:38 2.0K ncbiRefSeqCds.txt.gz 2018-02-09 14:05 208K ncbiRefSeqCds.sql 2018-02-09 14:05 1.4K ncbiRefSeq.txt.gz 2018-02-09 13:38 2.4M ncbiRefSeq.sql 2018-02-09 13:38 1.9K multiz8waySummary.txt.gz 2012-05-13 21:07 2.3M multiz8waySummary.sql 2012-05-13 21:07 1.5K multiz8wayFrames.txt.gz 2012-05-13 20:55 14M multiz8wayFrames.sql 2012-05-13 20:55 1.7K multiz8way.txt.gz 2012-05-13 20:58 37M multiz8way.sql 2012-05-13 20:58 1.5K mrnaOrientInfo.txt.gz 2020-08-19 09:22 27K mrnaOrientInfo.sql 2020-08-19 09:22 1.8K microsat.txt.gz 2015-08-23 16:39 158K microsat.sql 2015-08-23 16:39 1.5K intronEst.txt.gz 2019-03-17 09:26 7.8M intronEst.sql 2019-03-17 09:26 2.1K history.txt.gz 2012-05-13 20:51 1.0K history.sql 2012-05-13 20:51 1.5K hgFindSpec_pushedout.txt.gz 2023-12-05 13:51 1.2K hgFindSpec_pushedout.sql 2023-12-05 13:51 1.8K hgFindSpec.txt.gz 2023-12-05 13:51 1.2K hgFindSpec.sql 2023-12-05 13:51 1.8K grp.txt.gz 2014-03-02 03:40 208 grp.sql 2014-03-02 03:40 1.3K gold.txt.gz 2012-05-13 20:47 268K gold.sql 2012-05-13 20:47 1.6K genscan.txt.gz 2013-12-09 23:13 1.3M genscan.sql 2013-12-09 23:13 1.7K gc5BaseBw.txt.gz 2012-05-13 20:59 59 gc5BaseBw.sql 2012-05-13 20:59 1.2K gbLoaded.txt.gz 2020-08-19 09:27 41K gbLoaded.sql 2020-08-19 09:27 1.6K gap.txt.gz 2012-05-13 21:05 423K gap.sql 2012-05-13 21:05 1.5K extNcbiRefSeq.txt.gz 2018-02-09 14:05 86 extNcbiRefSeq.sql 2018-02-09 14:05 1.5K extFile.txt.gz 2012-05-13 21:05 75 extFile.sql 2012-05-13 21:05 1.3K estOrientInfo.txt.gz 2019-03-17 09:27 3.1M estOrientInfo.sql 2019-03-17 09:27 1.8K ensemblToGeneName.txt.gz 2019-02-10 03:41 164K ensemblToGeneName.sql 2019-02-10 03:41 1.4K ensemblSource.txt.gz 2019-02-10 03:41 80K ensemblSource.sql 2019-02-10 03:41 1.3K ensPep.txt.gz 2019-02-10 03:41 7.3M ensPep.sql 2019-02-10 03:41 1.3K ensGtp.txt.gz 2019-02-10 03:41 295K ensGtp.sql 2019-02-10 03:41 1.4K ensGene.txt.gz 2019-02-10 03:41 2.1M ensGene.sql 2019-02-10 03:41 1.9K cytoBandIdeo.txt.gz 2013-04-28 15:14 33K cytoBandIdeo.sql 2013-04-28 15:14 1.5K cpgIslandExtUnmasked.txt.gz 2019-04-14 03:21 1.0M cpgIslandExtUnmasked.sql 2019-04-14 03:21 1.7K cpgIslandExt.txt.gz 2019-04-14 03:21 726K cpgIslandExt.sql 2019-04-14 03:21 1.7K chromInfo.txt.gz 2012-05-13 20:55 33K chromInfo.sql 2012-05-13 20:55 1.3K chromAlias.txt.gz 2019-02-10 03:41 66K chromAlias.sql 2019-02-10 03:41 1.4K chainXenTro9Link.txt.gz 2017-12-14 10:20 47M chainXenTro9Link.sql 2017-12-14 10:20 1.5K chainXenTro9.txt.gz 2017-12-14 10:20 12M chainXenTro9.sql 2017-12-14 10:20 1.7K chainTetNig2Link.txt.gz 2012-05-13 20:58 106M chainTetNig2Link.sql 2012-05-13 20:57 1.5K chainTetNig2.txt.gz 2012-05-13 21:04 12M chainTetNig2.sql 2012-05-13 21:04 1.6K chainOryLat2Link.txt.gz 2012-05-13 20:56 185M chainOryLat2Link.sql 2012-05-13 20:55 1.5K chainOryLat2.txt.gz 2012-05-13 20:49 32M chainOryLat2.sql 2012-05-13 20:49 1.6K chainOreNil1Link.txt.gz 2012-05-13 21:02 189M chainOreNil1Link.sql 2012-05-13 21:01 1.5K chainOreNil1.txt.gz 2012-05-13 20:47 31M chainOreNil1.sql 2012-05-13 20:47 1.6K chainMm10Link.txt.gz 2013-08-04 13:03 31M chainMm10Link.sql 2013-08-04 13:03 1.5K chainMm10.txt.gz 2013-08-04 13:03 4.7M chainMm10.sql 2013-08-04 13:03 1.7K chainLatCha1Link.txt.gz 2012-05-13 21:05 41M chainLatCha1Link.sql 2012-05-13 21:05 1.5K chainLatCha1.txt.gz 2012-05-13 21:04 10M chainLatCha1.sql 2012-05-13 21:04 1.6K chainGasAcu1Link.txt.gz 2012-05-13 20:53 182M chainGasAcu1Link.sql 2012-05-13 20:53 1.5K chainGasAcu1.txt.gz 2012-05-13 21:06 29M chainGasAcu1.sql 2012-05-13 21:06 1.6K chainGalGal6Link.txt.gz 2019-01-20 08:23 30M chainGalGal6Link.sql 2019-01-20 08:23 1.5K chainGalGal6.txt.gz 2019-01-20 08:23 5.2M chainGalGal6.sql 2019-01-20 08:23 1.7K chainGadMor1Link.txt.gz 2012-05-13 20:52 92M chainGadMor1Link.sql 2012-05-13 20:52 1.5K chainGadMor1.txt.gz 2012-05-13 20:47 21M chainGadMor1.sql 2012-05-13 20:47 1.6K chainDanRer7Link.txt.gz 2012-05-13 21:05 109M chainDanRer7Link.sql 2012-05-13 21:05 1.5K chainDanRer7.txt.gz 2012-05-13 21:06 28M chainDanRer7.sql 2012-05-13 21:06 1.6K bigFiles.txt.gz 2024-04-14 03:31 90 bigFiles.sql 2024-04-14 03:31 1.4K augustusGene.txt.gz 2015-07-26 13:38 2.4M augustusGene.sql 2015-07-26 13:38 1.9K all_mrna.txt.gz 2020-05-06 13:45 75K all_mrna.sql 2020-05-06 13:45 2.1K all_est.txt.gz 2019-03-17 09:27 13M all_est.sql 2019-03-17 09:27 2.1K